Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Phospholipid phosphatase 4.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_3 g4140 g4140.t7 TSS g4140.t7 30903892 30903892
chr_3 g4140 g4140.t7 isoform g4140.t7 30904128 30906789
chr_3 g4140 g4140.t7 exon g4140.t7.exon1 30904128 30904267
chr_3 g4140 g4140.t7 cds g4140.t7.CDS1 30904128 30904267
chr_3 g4140 g4140.t7 exon g4140.t7.exon2 30905882 30905939
chr_3 g4140 g4140.t7 cds g4140.t7.CDS2 30905882 30905939
chr_3 g4140 g4140.t7 exon g4140.t7.exon3 30906000 30906111
chr_3 g4140 g4140.t7 cds g4140.t7.CDS3 30906000 30906111
chr_3 g4140 g4140.t7 exon g4140.t7.exon4 30906179 30906209
chr_3 g4140 g4140.t7 cds g4140.t7.CDS4 30906179 30906209
chr_3 g4140 g4140.t7 exon g4140.t7.exon5 30906265 30906507
chr_3 g4140 g4140.t7 cds g4140.t7.CDS5 30906265 30906507
chr_3 g4140 g4140.t7 exon g4140.t7.exon6 30906581 30906789
chr_3 g4140 g4140.t7 cds g4140.t7.CDS6 30906581 30906599
chr_3 g4140 g4140.t7 TTS g4140.t7 30906883 30906883

Sequences

>g4140.t7 Gene=g4140 Length=793
ATGCTACGAAATATAAAATCTAAAATATACATATGGATTGAAATTATTATAAGGCTTGCT
CTCTTTGTAGCTTTTTTGAAATTAGAGACATTAGAGCCTTTTCAAAGGAAAATTTTAGCT
GATGATTTATGGAATTATCGTTATCCTAATAAAAAATCATACGTTCCAGTTACATTGTTA
TGGCCAATTCTCACTCTTATCCCAACTTTTGTGTTTATTTTAAATTATATTTTTACGAGA
CATTCAAAAGATTTAAAAGCAGCTATGCTTGGTCATACTTTAGCATTTGGACTTAATGGT
GTTTTAGTAGATATTATCAAACTTACTGTCGGTCGACCAAGACCTGATTTTTTTGAACGA
TGTTGGCCAGACGGAATAATGAATTCTGAAATGATATGCACAGGAGAATATTGGTCAGTT
TTGGATGGCAGGAAAAGTTTCCCGAGCGGTCATTCCTCATTCTCATTCGCTAGTTTAGGA
TTTTTGACTTTTTATTTAATTGGAAAGTTGAAAATATTTTCGGATGAAGGAAGAGGAAAC
AGTTTAAAACTTATAATTTCATTTTTTCCTTTTATTGTTGCCATCAATATCAAGAACATG
TGACTATCATCATTGGAAAGAAGATGTTGTCGTTGGAAGTTTAATTGGTATTTTAATTGC
ATATTTATGCTATCGACAATTTTTTCCACCACTTGCGAGTAAAAAATCAAATTTATGCTA
TGAAATGCTTTACCATCTTTCTGCTACAAATGACTCAAATGATCTTCTCGAAAAAGACAT
TAAATGGATCTAA

>g4140.t7 Gene=g4140 Length=200
MLRNIKSKIYIWIEIIIRLALFVAFLKLETLEPFQRKILADDLWNYRYPNKKSYVPVTLL
WPILTLIPTFVFILNYIFTRHSKDLKAAMLGHTLAFGLNGVLVDIIKLTVGRPRPDFFER
CWPDGIMNSEMICTGEYWSVLDGRKSFPSGHSSFSFASLGFLTFYLIGKLKIFSDEGRGN
SLKLIISFFPFIVAINIKNM

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g4140.t7 CDD cd03390 PAP2_containing_1_like 44 195 4.44464E-54
7 g4140.t7 Gene3D G3DSA:1.20.144.10 - 3 197 1.4E-14
2 g4140.t7 PANTHER PTHR10165 LIPID PHOSPHATE PHOSPHATASE 10 197 5.4E-56
3 g4140.t7 PANTHER PTHR10165:SF87 PHOSPHOLIPID PHOSPHATASE 5 10 197 5.4E-56
1 g4140.t7 Pfam PF01569 PAP2 superfamily 93 195 3.3E-16
8 g4140.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 8 -
15 g4140.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 9 26 -
12 g4140.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 27 58 -
18 g4140.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 59 78 -
9 g4140.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 79 89 -
14 g4140.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 90 110 -
11 g4140.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 111 149 -
17 g4140.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 150 168 -
10 g4140.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 169 179 -
16 g4140.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 180 197 -
13 g4140.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 198 200 -
6 g4140.t7 SUPERFAMILY SSF48317 Acid phosphatase/Vanadium-dependent haloperoxidase 11 171 9.03E-23
4 g4140.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 9 26 -
5 g4140.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 57 79 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0042577 lipid phosphatase activity MF
GO:0046839 phospholipid dephosphorylation BP
GO:0006644 phospholipid metabolic process BP
GO:0008195 phosphatidate phosphatase activity MF

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below. There were no conditions that were differentially expressed